This place uses specials that have the price of toppings built in. I realize that I can set 0 as the price of the toppings but is there any way I can limit the amount of toppings the user is able to add per pizza or make it up charge as they pass that limit?

first of all, i think you are talking about the premium "add ingredients" extension. if this is the case, we should not really be talking about this here on the wordpress site , as this support forum is only intended for the free wppizza plugin

so , just send me an email to dev[at]wp-pizza.com and i'll reply that way (either way though you should be looking at the custom groups in that extension)